gloTK

GloTK is the Genomes of Luminous Organisms Toolkit. It contains scripts to facilitate genome assembly optomization and analysis using common genome assemblers.

Supported Assemblers

Currently there are only scripts for one assembler:

• Meraculous 2.2.2.4+

Dependencies

• The mer_reporter.py script currently requires the following to be installed:
  • Python 3.5
    • (If you haven't installed yet, I recommend the Anaconda distribution)
  • py-gfm
    • Python Github-flavored Markdown

Install

You can install the gloTK package on your linux machine by typing pip install gloTK in your terminal.

Major releases of gloTK are uploaded to the Python Package Index.

Scripts

To use these programs, install gloTK as described above and type glotk into your terminal. If you hit the tab key a few times your computer should try to autocomplete and you will see a few options:

• glotk-mer-reporter.py
  • Generates HTML reports of all Meraculous assemblies found within the current working directory (CWD). Collates all relevant files and images into a meraculous_reports directory in the CWD.
• glotk-sweep
  • This allows the user to input a single meraculous config file, and to define parameters to sweep on and optomize. Currently this program supports sweeping on mer_size and bubble_depth_threshold. Typing glotk-sweep into your terminal after installing will give you more details.

News

v0.1.15 - 20161116

• This version incorporates glotk-project. This script reads in a config file and generates a 'glotk_project' directory in which information about the libraries, assemblies, et cetera for this Meraculous genome project is stored. Assemblies, reports, config files, et cetera will take place in adjacent directories
• gloTK project files will now take on the following file structure:

project_dir/
|--glotk_info/
|  |  default_config.config
|  |  sample_metadata.config
|  |  read_metadata.config
|  |  assemblynumber_to_runname.txt
|  |
|  |--activity_log/
|  |     as000.log
|  |     as001.log
|  |     etcetera.log
|  |
|  |--read_configs/
|        reads0.yaml #this is the initial yaml file for imported reads
|        reads1.yaml #reads generated from Seqprep, trimmomatic, et cetera
|
|--glotk_assemblies
|  |--as000_<assembly_name>/
|  |  |--assembler_output/
|  |
|  |--as001_20161102_ME_pleu_bach_k63_d1/
|     |--meraculous_etcetera
|
|--glotk_configs
|     as000_<assembly_name>.config
|     as001_20161102_ME_pleu_bach_k63_d1.config
|
|--glotk_reads
|  |  reads.log
|  |
|  |--reads0/
|  |     <forward_reads_symlink>.fq.gz
|  |     <reverse_reads_symlink>.fq.gz
|  |
|  |--reads1/
|        <processed_forward>.fq.gz
|        <processed_reverse>.fq.gz
|
|--glotk_fastqc
|--glotk_kmers
|--glotk_reports

v0.1.14 - 20161102

• Gave a --triplet flag to glotk-sweep to cause the assembler to run diploid modes 0, 1, and 2 on the same kmer size.

v0.1.13 - 20161102

• Made glotk-sweep function by inputting each value of k to assemble for, rather than using 'sweep start', 'sweep stop', and 'sweep interval'. Usage is: '--slist 23 27 57' to perform assemblies for those three values